Sandbox 45

= Trypsin =

PDB ID#:3LJJ The various interactive tendencies and chemical characteristics of amino acids in this serine protease contribute to the protein's structure and catalytic function. The spacial arrangement of Trypsin's 223 residues in relation to themselves and their aqueous environment is displayed below.

Structure
Bovine Trypsin contains three alpha helices of lengths 3, 7, and 13 residues. Two beta sheets, A and B, are comprised of 7 and 6 strands. B is the only true beta barrel, though both appear similar to the motif. In the native conformation, regular and non-regular secondary structures interact with itself in numerous ways, achieving the lowest energy tertiary structure.

The distribution of hydrophilic (green) and hydrophobic (yellow) residues is one of the most important aspects of protein's primary sequence. The protein as a whole achieves its native conformation primarily by the hydrophobic collapse of supersecondary structures; hydrophobic side chains are internalized while water molecules interact with the water-soluble side chains pushed to the exterior. Water interaction (red) with the surface of the protein shows this, as a transparent view shows an absence of water within the hydrophobic core.

A closer look at the helix dangling at the end of the peptide chain shows hydrogen bonding and water bridges between the helix and local residues of the remaining peptide. More significantly, residues undergo van der Waals interactions. It's not the force of these interactions that holds the helix in place, but the entropy change to water when these hydrophobic residues interact with each other rather than the polar solvent. 

Because of its role in metabolism, disulfide bonds also significantly contribute to the stability of the protein. Typically, proteins in an extra-cellular, oxidizing environment contain disulfide bonds that hold the structure together through variable temperature and pH. It follows that trypsin, a digestive protease found in the digestive tract, would require this added stability.

The sequence of trypsin is variable from species to species to an extent, because the secondary/tertiary structure and function can remain despite some changes in primary structure. Particular amino acids exist in a range of possible variability. Blue represents highly variability, red represents conserved amino acids.

Ligand Binding and Catalysis
The structure of this particular bovine trypsin was determined in complex with ligand 10U, formula C20H29N5O2, along with two sulfate ions (highlighted) and a Calcium ion (green). Four key amino acids interact with Calcium at a subsite loop. The binding of ligand 10U involves water bridges, direct hydrogen bonding , and a host of <scene name='Sandbox_45/Ligandhydrophobic/1'>hydrophobic interactions. The figure below shows this binding in two dimensions.

The binding of trypsin to ligand 10U somewhat emulates the binding to its specific peptide substrates. The preference for lysine or arginine in trypsin catalysis is due to the composition of the trypsin <scene name='Sandbox_45/Specificitypocketasp189gly216/2'>specificity pocket. Here (green), Asp 189 and one of two significant glycine backbones, Gly 216, interact with the ligand as they would with Arg or Lys.

The <scene name='Sandbox_45/Ctriadd102h57s195/4'>catalytic triad ; Asp 102, His 57, and Ser 195, shown here in yellow, is positioned near the substrate. The catalytically active histidine and serine side chains are even near an amide bond in 10U, just like the amide bond broken in peptide hydrolysis. According to FirstGlance in Jmol, there is no bonding of these groups with the ligand, apart from minor van der Waal's interactions with Hist 57. If Ligand 10U were a transition state analog, some covalent connection would exist in addition to hydrogen bonds. 10U simulates the substrate, but does not hydrolyze at either of its two amide bonds, likely due to the local cyclic groups atypical of peptide backbones.

Regulation
Trypsin has long been known as unique in that it is an allosterically regulated monomer. In viewing the 3D structure, the allosteric sight appears to most likely be the subsite loop, which can bind Calcium. New research involving structural comparisons of trypsin-like serine proteases bound and unbound to Calcium and other effectors is being done to better understand the mechanism of this regulation.

In order for trypsin to be synthesized in the pancreas without the hydrolysis of pancreatic tissue, it must first be synthesized as the zymogen trypsinogen. When the molecule is in the digestive tract, away from the proteins it's not supposed to hydrolyze, the Lys15-<scene name='Sandbox_45/Ile16/1'>Ile16 bond is cleaved first by mucous secretions and then by newly activated trypsin itself.